Hi Bjoern, Yes, I do:
java -version
java version "1.7.0_85" OpenJDK Runtime Environment (IcedTea 2.6.1) (7u85-2.6.1-5ubuntu0.14.04.1) OpenJDK 64-Bit Server VM (build 24.85-b03, mixed mode)
Can it be related that my API key has change while migrating to Postgresql? I tried to put it back the old one in *galaxy.ini*, but Galaxy does not pick it from *master_api_key*.
Thank you in advance.
Mic
On Tue, Nov 17, 2015 at 12:28 PM, Björn Grüning bjoern.gruening@gmail.com wrote:
Hi Mic,
do you have Java installed?
cheers, Bjoern
Am 17.11.2015 um 02:05 schrieb Mic:
Hello, I installed FastQC (~/shed_tools/toolshed.g2.bx.psu.edu/repos/*devteam* /fastqc/*2d094334f61e*/
*FastQC ).* However, I got the following error while running it:
*Fatal error: Exit code 1 () Traceback (most recent call last): File "/home/lorencm/shed_tools/
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFastQC.py
<
http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFas...
", line 157, in <module> assert
os.path.isfile(opts.executable),'##rgFastQC.py
error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /fastqc*
The Fastqc package seems to be correctly installed:
*~/galaxy/tool_dependency/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0
ls -1 -ahltotal 824Kdrwxrwxr-x 8 lorencm lorencm 4.0K Nov 4 02:21
.drwxrwxr-x 3 lorencm lorencm 4.0K Nov 4 02:21 ..drwxrwxr-x 2 lorencm lorencm 4.0K Nov 4 02:21 Configuration-rwxrwxr-x 1 lorencm lorencm 251 Nov 4 02:21 env.sh-rwxr-xr-x 1 lorencm lorencm 13K Nov 4 02:21 fastqc-rw-rw-r-- 1 lorencm lorencm 2.2K Nov 4 02:21 fastqc_icon.icodrwxrwxr-x 5 lorencm lorencm 4.0K Nov 4 02:21 Help-rw-rw-r-- 1 lorencm lorencm 5.5K Nov 4 02:21 INSTALL.txt-rw-rw-r--
1
lorencm lorencm 49K Nov 4 02:21 jbzip2-0.9.jar-rw-rw-r-- 1 lorencm lorencm 35K Nov 4 02:21 LICENSE.txtdrwxrwxr-x 3 lorencm lorencm 4.0K
Nov
4 02:21 netdrwxrwxr-x 3 lorencm lorencm 4.0K Nov 4 02:21 org-rw-rw-r-- 1 lorencm lorencm 2.1K Nov 4 02:21 README.txt-rw-rw-r-- 1 lorencm lorencm 32K Nov 4 02:21 RELEASE_NOTES.txt-rw-rw-r-- 1 lorencm lorencm 101 Nov
4
02:21 run_fastqc.bat-rw-rw-r-- 1 lorencm lorencm 630K Nov 4 02:21 sam-1.103.jardrwxrwxr-x 3 lorencm lorencm 4.0K Nov 4 02:21 Templatesdrwxrwxr-x 3 lorencm lorencm 4.0K Nov 4 02:21 uk* What do I miss out?
Thank you in advance.
Mic
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